Structure

Physi-Chem Properties

Molecular Weight:  76.05
Volume:  78.025
LogP:  -1.023
LogD:  -1.387
LogS:  0.85
# Rotatable Bonds:  2
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.459
Synthetic Accessibility Score:  2.346
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.444
MDCK Permeability:  0.00220667477697134
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.079
20% Bioavailability (F20%):  0.184
30% Bioavailability (F30%):  0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.266
Plasma Protein Binding (PPB):  9.324545860290527%
Volume Distribution (VD):  0.82
Pgp-substrate:  93.69273376464844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.191
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.147
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.115
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.098
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.108

ADMET: Excretion

Clearance (CL):  5.94
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.072
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.674
Carcinogencity:  0.115
Eye Corrosion:  0.962
Eye Irritation:  0.995
Respiratory Toxicity:  0.055

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC236761

Natural Product ID:  NPC236761
Common Name*:   1,3-Propanediol
IUPAC Name:   propane-1,3-diol
Synonyms:   1,3-Propanediol
Standard InCHIKey:  YPFDHNVEDLHUCE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H8O2/c4-2-1-3-5/h4-5H,1-3H2
SMILES:  OCCCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL379652
PubChem CID:   10442
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0000286] Primary alcohols

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1039/C8GC03728K]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[11914965]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[20929806]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21268200]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22544021]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22851214]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22909174]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23113661]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23727191]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23864262]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26062534]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26358188]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26488898]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26951651]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[27116034]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[27825357]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29077207]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29096626]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[29667821]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30061932]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30496827]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30684358]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[32830192]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[33195815]
NPO41850 A new engineered strain of Escherichia coli [n.a.] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[34824227]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT27 Others Unspecified log Ks = 0.67 n.a. PMID[467972]
NPT2 Others Unspecified Kcat/Km = 1.71 /M/s PMID[467973]
NPT2 Others Unspecified Km = 23640000.0 nM PMID[467973]
NPT2 Others Unspecified Kcat = 0.041 /s PMID[467973]
NPT2 Others Unspecified Potency n.a. 40333.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 81189.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 80476.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 25674.5 nM PubChem BioAssay data set

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC236761 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8421 Intermediate Similarity NPC311000
0.8182 Intermediate Similarity NPC157340
0.8182 Intermediate Similarity NPC94144
0.8182 Intermediate Similarity NPC87529
0.8095 Intermediate Similarity NPC219266
0.7826 Intermediate Similarity NPC88887
0.7619 Intermediate Similarity NPC294703
0.7391 Intermediate Similarity NPC199270
0.7391 Intermediate Similarity NPC114270
0.7273 Intermediate Similarity NPC299484
0.7273 Intermediate Similarity NPC110344
0.7273 Intermediate Similarity NPC88839
0.72 Intermediate Similarity NPC320326
0.7143 Intermediate Similarity NPC163707
0.7083 Intermediate Similarity NPC213764
0.7083 Intermediate Similarity NPC140389
0.7083 Intermediate Similarity NPC82694
0.7 Intermediate Similarity NPC149567
0.6957 Remote Similarity NPC52403
0.6957 Remote Similarity NPC39977
0.6923 Remote Similarity NPC33415
0.6923 Remote Similarity NPC301586
0.6842 Remote Similarity NPC2724
0.6667 Remote Similarity NPC245688
0.6667 Remote Similarity NPC34153
0.6667 Remote Similarity NPC256186
0.6667 Remote Similarity NPC23071
0.64 Remote Similarity NPC275462
0.64 Remote Similarity NPC304786
0.64 Remote Similarity NPC190797
0.64 Remote Similarity NPC232554
0.6207 Remote Similarity NPC321170
0.6207 Remote Similarity NPC187058
0.6207 Remote Similarity NPC313303
0.6207 Remote Similarity NPC127074
0.6207 Remote Similarity NPC197207
0.6207 Remote Similarity NPC31433
0.6207 Remote Similarity NPC182541
0.6207 Remote Similarity NPC266566
0.6207 Remote Similarity NPC149070
0.6154 Remote Similarity NPC252154
0.6154 Remote Similarity NPC560
0.6154 Remote Similarity NPC128335
0.6071 Remote Similarity NPC327718
0.6071 Remote Similarity NPC270334
0.6 Remote Similarity NPC237965
0.6 Remote Similarity NPC318912
0.5926 Remote Similarity NPC39869
0.5926 Remote Similarity NPC276332
0.5926 Remote Similarity NPC272307
0.5926 Remote Similarity NPC324353
0.5862 Remote Similarity NPC198126
0.5714 Remote Similarity NPC159845
0.5714 Remote Similarity NPC325345
0.5714 Remote Similarity NPC238135
0.5714 Remote Similarity NPC52362
0.5714 Remote Similarity NPC279895
0.5714 Remote Similarity NPC261397
0.5667 Remote Similarity NPC317060
0.5625 Remote Similarity NPC66052
0.5625 Remote Similarity NPC86412
0.5625 Remote Similarity NPC168052
0.5625 Remote Similarity NPC250870
0.5625 Remote Similarity NPC192065
0.5625 Remote Similarity NPC325034
0.5625 Remote Similarity NPC293908
0.5625 Remote Similarity NPC191084

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC236761 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8421 Intermediate Similarity NPD8223 Approved
0.8182 Intermediate Similarity NPD8226 Approved
0.7391 Intermediate Similarity NPD8225 Phase 3
0.7143 Intermediate Similarity NPD8224 Approved
0.7083 Intermediate Similarity NPD8207 Approved
0.7 Intermediate Similarity NPD7374 Approved
0.6923 Remote Similarity NPD8549 Clinical (unspecified phase)
0.64 Remote Similarity NPD8231 Approved
0.6207 Remote Similarity NPD8557 Approved
0.6207 Remote Similarity NPD8558 Approved
0.6207 Remote Similarity NPD8814 Phase 3
0.6207 Remote Similarity NPD8237 Approved
0.5862 Remote Similarity NPD8236 Phase 1
0.5862 Remote Similarity NPD8234 Approved
0.5862 Remote Similarity NPD8618 Approved
0.5862 Remote Similarity NPD8235 Approved
0.5833 Remote Similarity NPD8196 Approved
0.5714 Remote Similarity NPD8988 Clinical (unspecified phase)
0.5625 Remote Similarity NPD9053 Approved
0.5625 Remote Similarity NPD9051 Approved
0.5625 Remote Similarity NPD9112 Discontinued
0.5625 Remote Similarity NPD9052 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data